Rarefaction Plot

Rarefaction Plot

Usage

# S4 method for class 'RarefactionIndex,missing'
plot(
  x,
  color = NULL,
  symbol = FALSE,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topleft"),
  ...
)

Arguments

x

A RarefactionIndex object to be plotted.

color

A vector of colors (will be mapped to the rownames of object). If color is a named a named vector, then the colors will be associated with the rownames of object. Ignored if set to FALSE.

symbol

A specification for the line type (will be mapped to the names of x). If symbol is a named a named vector, then the line types will be associated with the names of x. Ignored if set to FALSE.

main

A character string giving a main title for the plot.

sub

A character string giving a subtitle for the plot.

ann

A logical scalar: should the default annotation (title and x, y and z axis labels) appear on the plot?

axes

A logical scalar: should axes be drawn on the plot?

frame.plot

A logical scalar: should a box be drawn around the plot?

panel.first

An an expression to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids.

panel.last

An expression to be evaluated after plotting has taken place but before the axes, title and box are added.

legend

A list of additional arguments to be passed to graphics::legend(); names of the list are used as argument names. If NULL, no legend is displayed.

...

Further graphical parameters to be passed to graphics::lines().

Value

plot() is called for its side-effects: it results in a graphic being displayed (invisibly returns x).

See also

Other diversity measures: heterogeneity(), occurrence(), plot_diversity, profiles(), rarefaction(), richness(), she(), similarity(), simulate(), turnover()

Author

N. Frerebeau

Examples

## Data from Conkey 1980, Kintigh 1989
data("cantabria")

## Replicate fig. 3 from Baxter 2011
rare <- rarefaction(cantabria, sample = 23, method = "baxter")
plot(rare, panel.first = graphics::grid())


## Change graphical parameters
plot(rare, color = color("bright")(5), symbol = 1:5)